Starting phenix.real_space_refine on Thu Mar 5 05:40:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0n_24110/03_2026/7n0n_24110.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0n_24110/03_2026/7n0n_24110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n0n_24110/03_2026/7n0n_24110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0n_24110/03_2026/7n0n_24110.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n0n_24110/03_2026/7n0n_24110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0n_24110/03_2026/7n0n_24110.map" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.041 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12888 2.51 5 N 3276 2.21 5 O 3356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19632 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4908 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 1, 'ASP:plan': 6, 'GLU:plan': 8, 'TYR:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 117 Restraints were copied for chains: B, C, D Time building chain proxies: 3.94, per 1000 atoms: 0.20 Number of scatterers: 19632 At special positions: 0 Unit cell: (140.17, 140.17, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3356 8.00 N 3276 7.00 C 12888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 737.7 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 63.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.540A pdb=" N GLY A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.544A pdb=" N TYR A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 4.072A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.508A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.559A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.784A pdb=" N GLU A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.565A pdb=" N SER A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.643A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 414 removed outlier: 3.511A pdb=" N LEU A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.694A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 519 through 527 removed outlier: 3.973A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 560 removed outlier: 3.787A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 606 removed outlier: 5.423A pdb=" N GLU A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 651 removed outlier: 3.744A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 674 removed outlier: 3.817A pdb=" N TRP A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.540A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 removed outlier: 3.545A pdb=" N TYR B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 4.072A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.508A pdb=" N LEU B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.559A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.785A pdb=" N GLU B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.565A pdb=" N SER B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.642A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 414 removed outlier: 3.510A pdb=" N LEU B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 470 through 492 Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.694A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 519 through 527 removed outlier: 3.973A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 560 removed outlier: 3.787A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 606 removed outlier: 5.424A pdb=" N GLU B 599 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 651 removed outlier: 3.743A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 674 removed outlier: 3.817A pdb=" N TRP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.540A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 removed outlier: 3.543A pdb=" N TYR C 98 " --> pdb=" O GLY C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 4.072A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.507A pdb=" N LEU C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.559A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.784A pdb=" N GLU C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.565A pdb=" N SER C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.643A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 414 removed outlier: 3.511A pdb=" N LEU C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 412 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 414 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 470 through 492 Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.694A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 519 through 527 removed outlier: 3.974A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 560 removed outlier: 3.787A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 547 " --> pdb=" O VAL C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 606 removed outlier: 5.424A pdb=" N GLU C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 651 removed outlier: 3.743A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 674 removed outlier: 3.817A pdb=" N TRP C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.540A pdb=" N GLY D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.544A pdb=" N TYR D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 4.072A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.509A pdb=" N LEU D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.559A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.784A pdb=" N GLU D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.565A pdb=" N SER D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.643A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 414 removed outlier: 3.511A pdb=" N LEU D 381 " --> pdb=" O PRO D 377 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR D 412 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN D 414 " --> pdb=" O VAL D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 470 through 492 Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.694A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 519 through 527 removed outlier: 3.974A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 560 removed outlier: 3.787A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 606 removed outlier: 5.423A pdb=" N GLU D 599 " --> pdb=" O ASP D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 651 removed outlier: 3.743A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 674 removed outlier: 3.816A pdb=" N TRP D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.904A pdb=" N HIS A 165 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 341 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 707 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.905A pdb=" N HIS B 165 " --> pdb=" O CYS B 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 341 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 707 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.904A pdb=" N HIS C 165 " --> pdb=" O CYS C 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.979A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 341 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 707 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.905A pdb=" N HIS D 165 " --> pdb=" O CYS D 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 341 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 707 " --> pdb=" O SER D 341 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5972 1.34 - 1.46: 3821 1.46 - 1.57: 10167 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 20132 Sorted by residual: bond pdb=" SD MET C 404 " pdb=" CE MET C 404 " ideal model delta sigma weight residual 1.791 1.741 0.050 2.50e-02 1.60e+03 4.02e+00 bond pdb=" SD MET A 404 " pdb=" CE MET A 404 " ideal model delta sigma weight residual 1.791 1.741 0.050 2.50e-02 1.60e+03 3.96e+00 bond pdb=" SD MET B 404 " pdb=" CE MET B 404 " ideal model delta sigma weight residual 1.791 1.742 0.049 2.50e-02 1.60e+03 3.92e+00 bond pdb=" SD MET D 404 " pdb=" CE MET D 404 " ideal model delta sigma weight residual 1.791 1.742 0.049 2.50e-02 1.60e+03 3.87e+00 bond pdb=" CB MET B 404 " pdb=" CG MET B 404 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 ... (remaining 20127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 26411 2.28 - 4.57: 774 4.57 - 6.85: 111 6.85 - 9.14: 40 9.14 - 11.42: 32 Bond angle restraints: 27368 Sorted by residual: angle pdb=" N VAL D 649 " pdb=" CA VAL D 649 " pdb=" C VAL D 649 " ideal model delta sigma weight residual 112.96 107.16 5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" N VAL B 649 " pdb=" CA VAL B 649 " pdb=" C VAL B 649 " ideal model delta sigma weight residual 112.96 107.16 5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" N VAL A 649 " pdb=" CA VAL A 649 " pdb=" C VAL A 649 " ideal model delta sigma weight residual 112.96 107.17 5.79 1.00e+00 1.00e+00 3.35e+01 angle pdb=" N VAL C 649 " pdb=" CA VAL C 649 " pdb=" C VAL C 649 " ideal model delta sigma weight residual 112.96 107.19 5.77 1.00e+00 1.00e+00 3.32e+01 angle pdb=" N VAL D 691 " pdb=" CA VAL D 691 " pdb=" C VAL D 691 " ideal model delta sigma weight residual 113.71 109.88 3.83 9.50e-01 1.11e+00 1.63e+01 ... (remaining 27363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 10326 16.45 - 32.90: 1142 32.90 - 49.36: 252 49.36 - 65.81: 28 65.81 - 82.26: 28 Dihedral angle restraints: 11776 sinusoidal: 4564 harmonic: 7212 Sorted by residual: dihedral pdb=" CA ILE C 529 " pdb=" C ILE C 529 " pdb=" N GLN C 530 " pdb=" CA GLN C 530 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ILE A 529 " pdb=" C ILE A 529 " pdb=" N GLN A 530 " pdb=" CA GLN A 530 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ILE D 529 " pdb=" C ILE D 529 " pdb=" N GLN D 530 " pdb=" CA GLN D 530 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 11773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2437 0.060 - 0.121: 582 0.121 - 0.181: 89 0.181 - 0.241: 22 0.241 - 0.302: 6 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CB VAL C 348 " pdb=" CA VAL C 348 " pdb=" CG1 VAL C 348 " pdb=" CG2 VAL C 348 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL B 348 " pdb=" CA VAL B 348 " pdb=" CG1 VAL B 348 " pdb=" CG2 VAL B 348 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB VAL A 348 " pdb=" CA VAL A 348 " pdb=" CG1 VAL A 348 " pdb=" CG2 VAL A 348 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 3133 not shown) Planarity restraints: 3372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 88 " 0.011 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C VAL B 88 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL B 88 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO B 89 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 88 " -0.011 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C VAL A 88 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 88 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A 89 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 88 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C VAL C 88 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL C 88 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO C 89 " 0.012 2.00e-02 2.50e+03 ... (remaining 3369 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4227 2.77 - 3.31: 18939 3.31 - 3.84: 33203 3.84 - 4.37: 35196 4.37 - 4.90: 58979 Nonbonded interactions: 150544 Sorted by model distance: nonbonded pdb=" OG SER A 557 " pdb=" O ALA D 411 " model vdw 2.243 3.040 nonbonded pdb=" O LEU C 513 " pdb=" OG1 THR C 516 " model vdw 2.270 3.040 nonbonded pdb=" O LEU A 513 " pdb=" OG1 THR A 516 " model vdw 2.271 3.040 nonbonded pdb=" O LEU B 513 " pdb=" OG1 THR B 516 " model vdw 2.271 3.040 nonbonded pdb=" O LEU D 513 " pdb=" OG1 THR D 516 " model vdw 2.271 3.040 ... (remaining 150539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.660 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20132 Z= 0.275 Angle : 1.013 11.420 27368 Z= 0.513 Chirality : 0.056 0.302 3136 Planarity : 0.006 0.039 3372 Dihedral : 14.980 82.262 7104 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.38 % Allowed : 1.35 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 2428 helix: -1.05 (0.12), residues: 1456 sheet: -2.58 (0.72), residues: 40 loop : -1.93 (0.17), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 458 TYR 0.010 0.002 TYR D 471 PHE 0.021 0.003 PHE D 472 TRP 0.022 0.002 TRP C 677 HIS 0.011 0.002 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00613 (20132) covalent geometry : angle 1.01339 (27368) hydrogen bonds : bond 0.11382 ( 1072) hydrogen bonds : angle 5.85768 ( 3120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.618 Fit side-chains REVERT: A 271 TYR cc_start: 0.8717 (t80) cc_final: 0.8370 (t80) REVERT: A 277 MET cc_start: 0.8832 (tpt) cc_final: 0.8494 (mmm) REVERT: A 372 MET cc_start: 0.8903 (tpp) cc_final: 0.8701 (tpp) REVERT: A 636 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9105 (mp) REVERT: B 270 MET cc_start: 0.8752 (tpt) cc_final: 0.8551 (tpp) REVERT: B 607 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6987 (tmm) REVERT: B 715 TRP cc_start: 0.8563 (t60) cc_final: 0.8046 (t60) REVERT: C 607 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7151 (tmm) REVERT: C 715 TRP cc_start: 0.8541 (t60) cc_final: 0.7956 (t60) REVERT: D 270 MET cc_start: 0.8768 (tpt) cc_final: 0.8544 (tpp) REVERT: D 607 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7256 (tmm) REVERT: D 715 TRP cc_start: 0.8539 (t60) cc_final: 0.7847 (t60) outliers start: 8 outliers final: 0 residues processed: 145 average time/residue: 0.0951 time to fit residues: 23.8923 Evaluate side-chains 122 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 259 ASN B 222 GLN B 259 ASN C 222 GLN C 259 ASN D 222 GLN D 259 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.062948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053826 restraints weight = 109766.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055245 restraints weight = 62287.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056218 restraints weight = 41154.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056896 restraints weight = 30023.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057335 restraints weight = 23662.382| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20132 Z= 0.153 Angle : 0.582 7.343 27368 Z= 0.292 Chirality : 0.037 0.131 3136 Planarity : 0.004 0.028 3372 Dihedral : 4.854 19.356 2656 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.19 % Allowed : 5.10 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2428 helix: 0.30 (0.13), residues: 1484 sheet: -2.60 (0.84), residues: 40 loop : -1.66 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 702 TYR 0.009 0.001 TYR D 471 PHE 0.011 0.001 PHE D 311 TRP 0.011 0.001 TRP C 677 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00332 (20132) covalent geometry : angle 0.58178 (27368) hydrogen bonds : bond 0.03879 ( 1072) hydrogen bonds : angle 4.09433 ( 3120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.504 Fit side-chains REVERT: A 271 TYR cc_start: 0.8502 (t80) cc_final: 0.8212 (t80) REVERT: A 277 MET cc_start: 0.9053 (tpt) cc_final: 0.8717 (mmm) REVERT: A 715 TRP cc_start: 0.8787 (t60) cc_final: 0.8567 (t60) REVERT: B 270 MET cc_start: 0.8996 (tpt) cc_final: 0.8721 (tpp) REVERT: B 715 TRP cc_start: 0.8703 (t60) cc_final: 0.7993 (t60) REVERT: C 271 TYR cc_start: 0.8605 (t80) cc_final: 0.8301 (t80) REVERT: C 715 TRP cc_start: 0.8718 (t60) cc_final: 0.8021 (t60) REVERT: D 270 MET cc_start: 0.8986 (tpt) cc_final: 0.8703 (tpp) outliers start: 4 outliers final: 4 residues processed: 138 average time/residue: 0.1004 time to fit residues: 24.1184 Evaluate side-chains 116 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 71 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 183 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 259 ASN A 316 GLN B 222 GLN B 259 ASN B 316 GLN C 259 ASN C 316 GLN D 222 GLN D 316 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.062763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053220 restraints weight = 108769.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054644 restraints weight = 62631.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055602 restraints weight = 41925.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056235 restraints weight = 31060.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056706 restraints weight = 24982.180| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20132 Z= 0.217 Angle : 0.661 9.077 27368 Z= 0.329 Chirality : 0.040 0.155 3136 Planarity : 0.004 0.027 3372 Dihedral : 4.817 19.704 2656 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2428 helix: 0.73 (0.13), residues: 1504 sheet: -2.87 (0.86), residues: 40 loop : -1.44 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.008 0.001 TYR C 471 PHE 0.016 0.002 PHE A 601 TRP 0.016 0.001 TRP C 677 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00473 (20132) covalent geometry : angle 0.66082 (27368) hydrogen bonds : bond 0.04072 ( 1072) hydrogen bonds : angle 4.11706 ( 3120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.709 Fit side-chains REVERT: A 271 TYR cc_start: 0.8609 (t80) cc_final: 0.8350 (t80) REVERT: B 270 MET cc_start: 0.9075 (tpt) cc_final: 0.8800 (tpp) REVERT: B 715 TRP cc_start: 0.8825 (t60) cc_final: 0.8347 (t60) REVERT: C 271 TYR cc_start: 0.8622 (t80) cc_final: 0.8323 (t80) REVERT: C 715 TRP cc_start: 0.8848 (t60) cc_final: 0.8363 (t60) REVERT: D 270 MET cc_start: 0.9084 (tpt) cc_final: 0.8806 (tpp) REVERT: D 715 TRP cc_start: 0.8827 (t60) cc_final: 0.8445 (t60) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1046 time to fit residues: 23.1163 Evaluate side-chains 110 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 191 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 241 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 259 ASN ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.062804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053188 restraints weight = 111024.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054581 restraints weight = 63642.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.055530 restraints weight = 43368.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056209 restraints weight = 32458.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.056671 restraints weight = 26148.723| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20132 Z= 0.260 Angle : 0.691 7.302 27368 Z= 0.346 Chirality : 0.041 0.149 3136 Planarity : 0.004 0.025 3372 Dihedral : 4.926 18.842 2656 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2428 helix: 0.82 (0.13), residues: 1480 sheet: -2.80 (0.57), residues: 84 loop : -1.34 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.010 0.001 TYR C 471 PHE 0.013 0.002 PHE C 407 TRP 0.030 0.002 TRP A 715 HIS 0.008 0.002 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00568 (20132) covalent geometry : angle 0.69069 (27368) hydrogen bonds : bond 0.04162 ( 1072) hydrogen bonds : angle 4.26867 ( 3120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.615 Fit side-chains REVERT: A 715 TRP cc_start: 0.8785 (t60) cc_final: 0.8223 (t60) REVERT: B 270 MET cc_start: 0.9055 (tpt) cc_final: 0.8773 (tpp) REVERT: B 715 TRP cc_start: 0.8858 (t60) cc_final: 0.8471 (t60) REVERT: C 715 TRP cc_start: 0.8871 (t60) cc_final: 0.8471 (t60) REVERT: D 270 MET cc_start: 0.9064 (tpt) cc_final: 0.8779 (tpp) REVERT: D 715 TRP cc_start: 0.8865 (t60) cc_final: 0.8407 (t60) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1044 time to fit residues: 22.3117 Evaluate side-chains 97 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 43 optimal weight: 0.0970 chunk 178 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 chunk 164 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 259 ASN C 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.055367 restraints weight = 105993.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.056785 restraints weight = 59993.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.057720 restraints weight = 39423.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.058329 restraints weight = 28924.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058815 restraints weight = 23256.637| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20132 Z= 0.105 Angle : 0.545 7.617 27368 Z= 0.262 Chirality : 0.037 0.128 3136 Planarity : 0.003 0.024 3372 Dihedral : 4.272 17.867 2656 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2428 helix: 1.23 (0.14), residues: 1484 sheet: -2.82 (0.54), residues: 84 loop : -1.41 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 392 TYR 0.007 0.001 TYR B 471 PHE 0.011 0.001 PHE D 540 TRP 0.012 0.001 TRP C 657 HIS 0.006 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00219 (20132) covalent geometry : angle 0.54499 (27368) hydrogen bonds : bond 0.03330 ( 1072) hydrogen bonds : angle 3.66858 ( 3120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.719 Fit side-chains REVERT: A 271 TYR cc_start: 0.8502 (t80) cc_final: 0.8220 (t80) REVERT: B 255 MET cc_start: 0.9198 (tpp) cc_final: 0.8990 (tpp) REVERT: B 270 MET cc_start: 0.8962 (tpt) cc_final: 0.8720 (tpp) REVERT: B 271 TYR cc_start: 0.8615 (t80) cc_final: 0.8319 (t80) REVERT: B 715 TRP cc_start: 0.8712 (t60) cc_final: 0.8277 (t60) REVERT: C 271 TYR cc_start: 0.8498 (t80) cc_final: 0.8227 (t80) REVERT: C 715 TRP cc_start: 0.8743 (t60) cc_final: 0.8283 (t60) REVERT: D 270 MET cc_start: 0.8972 (tpt) cc_final: 0.8725 (tpp) REVERT: D 271 TYR cc_start: 0.8590 (t80) cc_final: 0.8295 (t80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0950 time to fit residues: 25.0673 Evaluate side-chains 116 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 165 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 219 optimal weight: 30.0000 chunk 144 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 316 GLN D 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.055198 restraints weight = 109077.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056549 restraints weight = 64734.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057416 restraints weight = 44197.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.058041 restraints weight = 33586.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.058456 restraints weight = 27216.782| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20132 Z= 0.125 Angle : 0.556 9.236 27368 Z= 0.268 Chirality : 0.037 0.171 3136 Planarity : 0.003 0.024 3372 Dihedral : 4.178 17.347 2656 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2428 helix: 1.41 (0.14), residues: 1480 sheet: -2.89 (0.53), residues: 84 loop : -1.40 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 392 TYR 0.007 0.001 TYR A 515 PHE 0.018 0.001 PHE C 540 TRP 0.017 0.001 TRP A 715 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00278 (20132) covalent geometry : angle 0.55582 (27368) hydrogen bonds : bond 0.03349 ( 1072) hydrogen bonds : angle 3.66945 ( 3120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.609 Fit side-chains REVERT: A 271 TYR cc_start: 0.8479 (t80) cc_final: 0.8203 (t80) REVERT: B 270 MET cc_start: 0.8849 (tpt) cc_final: 0.8589 (tpp) REVERT: B 271 TYR cc_start: 0.8522 (t80) cc_final: 0.8209 (t80) REVERT: B 715 TRP cc_start: 0.8725 (t60) cc_final: 0.8226 (t60) REVERT: C 271 TYR cc_start: 0.8475 (t80) cc_final: 0.8212 (t80) REVERT: C 715 TRP cc_start: 0.8756 (t60) cc_final: 0.8218 (t60) REVERT: D 270 MET cc_start: 0.8863 (tpt) cc_final: 0.8611 (tpp) REVERT: D 271 TYR cc_start: 0.8530 (t80) cc_final: 0.8220 (t80) REVERT: D 715 TRP cc_start: 0.8731 (t60) cc_final: 0.8142 (t60) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1035 time to fit residues: 24.4284 Evaluate side-chains 113 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 203 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 22 optimal weight: 0.0770 chunk 228 optimal weight: 8.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.063469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.054245 restraints weight = 108376.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055608 restraints weight = 61492.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056531 restraints weight = 41468.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057145 restraints weight = 30470.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057612 restraints weight = 24443.858| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20132 Z= 0.154 Angle : 0.576 7.074 27368 Z= 0.282 Chirality : 0.038 0.134 3136 Planarity : 0.003 0.024 3372 Dihedral : 4.237 18.100 2656 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.17), residues: 2428 helix: 1.42 (0.13), residues: 1480 sheet: -3.50 (0.82), residues: 40 loop : -1.32 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 392 TYR 0.009 0.001 TYR C 515 PHE 0.015 0.001 PHE A 491 TRP 0.023 0.001 TRP A 715 HIS 0.006 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00340 (20132) covalent geometry : angle 0.57594 (27368) hydrogen bonds : bond 0.03446 ( 1072) hydrogen bonds : angle 3.78878 ( 3120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.652 Fit side-chains REVERT: A 271 TYR cc_start: 0.8580 (t80) cc_final: 0.8345 (t80) REVERT: B 270 MET cc_start: 0.8998 (tpt) cc_final: 0.8706 (tpp) REVERT: B 715 TRP cc_start: 0.8851 (t60) cc_final: 0.8323 (t60) REVERT: C 271 TYR cc_start: 0.8595 (t80) cc_final: 0.8341 (t80) REVERT: C 715 TRP cc_start: 0.8864 (t60) cc_final: 0.8319 (t60) REVERT: D 270 MET cc_start: 0.9008 (tpt) cc_final: 0.8714 (tpp) REVERT: D 715 TRP cc_start: 0.8817 (t60) cc_final: 0.8167 (t60) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1064 time to fit residues: 23.5286 Evaluate side-chains 108 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 108 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 129 optimal weight: 0.0670 chunk 199 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 overall best weight: 2.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055788 restraints weight = 109505.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.057096 restraints weight = 66383.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057982 restraints weight = 45788.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058551 restraints weight = 34752.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059000 restraints weight = 28515.482| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 20132 Z= 0.119 Angle : 0.555 7.352 27368 Z= 0.265 Chirality : 0.037 0.160 3136 Planarity : 0.003 0.028 3372 Dihedral : 4.107 18.228 2656 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2428 helix: 1.52 (0.14), residues: 1480 sheet: -2.94 (0.54), residues: 84 loop : -1.32 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 458 TYR 0.008 0.001 TYR A 515 PHE 0.014 0.001 PHE A 491 TRP 0.029 0.001 TRP A 715 HIS 0.006 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00262 (20132) covalent geometry : angle 0.55483 (27368) hydrogen bonds : bond 0.03261 ( 1072) hydrogen bonds : angle 3.64303 ( 3120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.771 Fit side-chains REVERT: B 270 MET cc_start: 0.8813 (tpt) cc_final: 0.8540 (tpp) REVERT: B 271 TYR cc_start: 0.8525 (t80) cc_final: 0.8189 (t80) REVERT: B 607 MET cc_start: 0.7460 (ttp) cc_final: 0.6834 (tmm) REVERT: B 715 TRP cc_start: 0.8673 (t60) cc_final: 0.8245 (t60) REVERT: C 271 TYR cc_start: 0.8447 (t80) cc_final: 0.8105 (t80) REVERT: C 715 TRP cc_start: 0.8718 (t60) cc_final: 0.8256 (t60) REVERT: D 270 MET cc_start: 0.8822 (tpt) cc_final: 0.8549 (tpp) REVERT: D 271 TYR cc_start: 0.8521 (t80) cc_final: 0.8192 (t80) REVERT: D 715 TRP cc_start: 0.8721 (t60) cc_final: 0.8131 (t60) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1037 time to fit residues: 24.7121 Evaluate side-chains 109 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 11 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 226 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.064354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055186 restraints weight = 108914.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056540 restraints weight = 65264.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.057439 restraints weight = 44621.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058075 restraints weight = 33690.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058491 restraints weight = 27209.939| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20132 Z= 0.130 Angle : 0.560 7.281 27368 Z= 0.270 Chirality : 0.037 0.134 3136 Planarity : 0.003 0.028 3372 Dihedral : 4.093 18.329 2656 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.17), residues: 2428 helix: 1.56 (0.14), residues: 1480 sheet: -2.94 (0.54), residues: 84 loop : -1.26 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 458 TYR 0.009 0.001 TYR C 515 PHE 0.013 0.001 PHE A 491 TRP 0.030 0.001 TRP A 715 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00289 (20132) covalent geometry : angle 0.56015 (27368) hydrogen bonds : bond 0.03285 ( 1072) hydrogen bonds : angle 3.69886 ( 3120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.776 Fit side-chains REVERT: B 270 MET cc_start: 0.8913 (tpt) cc_final: 0.8619 (tpp) REVERT: B 271 TYR cc_start: 0.8553 (t80) cc_final: 0.8220 (t80) REVERT: B 641 LEU cc_start: 0.9376 (mm) cc_final: 0.9146 (pp) REVERT: B 715 TRP cc_start: 0.8752 (t60) cc_final: 0.8279 (t60) REVERT: C 271 TYR cc_start: 0.8511 (t80) cc_final: 0.8216 (t80) REVERT: C 641 LEU cc_start: 0.9376 (mm) cc_final: 0.9159 (pp) REVERT: C 715 TRP cc_start: 0.8789 (t60) cc_final: 0.8305 (t60) REVERT: D 270 MET cc_start: 0.8914 (tpt) cc_final: 0.8620 (tpp) REVERT: D 271 TYR cc_start: 0.8549 (t80) cc_final: 0.8218 (t80) REVERT: D 641 LEU cc_start: 0.9379 (mm) cc_final: 0.9165 (pp) REVERT: D 715 TRP cc_start: 0.8777 (t60) cc_final: 0.8216 (t60) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1062 time to fit residues: 24.1877 Evaluate side-chains 110 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 5 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 ASN C 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.052809 restraints weight = 108821.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054148 restraints weight = 64377.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055056 restraints weight = 43385.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.055669 restraints weight = 32373.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056074 restraints weight = 26003.054| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20132 Z= 0.246 Angle : 0.700 7.060 27368 Z= 0.346 Chirality : 0.042 0.159 3136 Planarity : 0.004 0.030 3372 Dihedral : 4.662 19.538 2656 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2428 helix: 1.11 (0.13), residues: 1500 sheet: -3.05 (0.53), residues: 84 loop : -1.10 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 458 TYR 0.014 0.001 TYR A 515 PHE 0.025 0.002 PHE D 456 TRP 0.041 0.002 TRP A 715 HIS 0.007 0.002 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00538 (20132) covalent geometry : angle 0.69993 (27368) hydrogen bonds : bond 0.04096 ( 1072) hydrogen bonds : angle 4.22636 ( 3120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.604 Fit side-chains REVERT: B 270 MET cc_start: 0.8955 (tpt) cc_final: 0.8633 (tpp) REVERT: B 715 TRP cc_start: 0.8820 (t60) cc_final: 0.8478 (t60) REVERT: C 715 TRP cc_start: 0.8839 (t60) cc_final: 0.8465 (t60) REVERT: D 270 MET cc_start: 0.8980 (tpt) cc_final: 0.8669 (tpp) REVERT: D 715 TRP cc_start: 0.8874 (t60) cc_final: 0.8421 (t60) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0963 time to fit residues: 19.5949 Evaluate side-chains 97 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 61 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 chunk 213 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 217 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 139 optimal weight: 0.3980 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055751 restraints weight = 106495.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.057158 restraints weight = 62963.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.058112 restraints weight = 42661.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058793 restraints weight = 31898.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.059251 restraints weight = 25565.243| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20132 Z= 0.098 Angle : 0.565 8.407 27368 Z= 0.265 Chirality : 0.037 0.129 3136 Planarity : 0.003 0.030 3372 Dihedral : 4.099 19.815 2656 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2428 helix: 1.51 (0.14), residues: 1476 sheet: -2.85 (0.55), residues: 84 loop : -1.32 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 684 TYR 0.009 0.001 TYR D 515 PHE 0.018 0.001 PHE C 540 TRP 0.031 0.001 TRP A 715 HIS 0.006 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00211 (20132) covalent geometry : angle 0.56518 (27368) hydrogen bonds : bond 0.03251 ( 1072) hydrogen bonds : angle 3.66370 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.12 seconds wall clock time: 38 minutes 28.03 seconds (2308.03 seconds total)